Collaborative github in Rstudio
MozFest2016, London, Sat 29 Oct. 1:00 - 3:00 pm
Open Science, Floor 9 - 903
Anna Krystalli @annakrystalli | Sharada Prasanna Mohanty @MeMohanty
handout: https://annakrystalli.github.io/Mozfest_github-rstudio/index.html
Session Roadmap
1 Introductions
- get to know the audience (10 mis)
- Shout outs and twitter polls.
- get to know github (25 mins)
- github as a computational research tool
2 Get stuck in
- Version control with github and rstudio (40 mins)
In this session, we are going to get you started with using version control from within RStudio.
The material is self-paced and includes a worked-example. It is suggested that you work through the sections in order.
- Collaborative github through rstudio #EvoLottery (40 mins)
In this exercise, each participant will fork a github repo, and contribute a file required to simulate the evolutionary trajectory of an imaginary species’ body size.
We’ll use github to collate all species files and plot them all up together at the end! We’ll also discover the skull and beak shapes associated with each simulated species size.
introductions: get to know the audience
Check #EvoLottery tweets for live twitter polls!
introductions: get to know github
version control and computing
"The need for a logical way to organize and control revisions has existed for almost as long as writing has existed, but revision control became much more important, and complicated, when the era of computing began."
version control and science
long been used to maintain code repositories in the software industry
especially in open source software
science increasingly computational
demands for increased openness and transparency
http://billmills.github.io/scienceXpython/
modern science workflows
can be overwhelming
succesful modern science workflows
can be extremely powerful
github for science
ideal for managing the full suite of research outputs such as datasets, statistical code, figures, lab notes, and manuscripts.
more on github for science
Github as part of Good Enough Practices in Scientific Computing
e.g My research workflow, based on Github by Carl Boettiger
Rstudio for r users
♡
invest in next generation science skills
…and super-charge your teams!
…or get left behind
why github?
empowers collaboration
repos
centralising information e.g. ROpenSci / rfishbase
issues
project management
commits
project tracking
fosters reproducibility
commits
traceability
entire process of project evolution reproducible
PRACTICALS
Practical 1: Github & Rstudio for version control
Code Cafe Style tutorial by Mike Croucher that will get you set up with all required software and able to link rstudio projects to github repos.
Enter Practical
Practical 2: Github & Rstudio for collaborative coding
#EvoLottery
Beak and skull shapes in birds of prey (“raptors”) are strongly coupled and largely controlled by size.
- In this exercise, each participant will fork a github repo, and contribute a file required to simulate the evolutionary trajectory of an imaginary species’ body size.
- We’ll use github to collate all species files and plot them all up together at the end! We’ll also discover the skull and beak shapes associated with each simulated species size.
Enter Practical